Ok, I've been living with this issue for quite a while now and nothings been solved so...
On one of my Klingon toons and now one of my Fed toons I have hit T3 Diplomacy/Marauding.
I COLLECTED my reward duty officer from the store in both cases, and got my tier commendation.
However, I have not unlocked the appropriate abilities for T3. Each of these toons have not gained the T3 transwarp abilities, nor unlocked the power to grant DI/Marauding.
Now, I have 4 other toons that have successfully gained all these powers. Both of these toons have been at T3 for at least 2 months, so I have logged out/back in numerous times. The problem persists and the abilities continue to be unavailable.
Go back through this forum.. many many other posts on the same topic, think there might even have been some on tribble during the december testing of S5 (not sure). This is just like a lot of other old stuff that goes unfixed.
If you see any feature that is working at present that you can unlock, then unlock it right away... it will break or get changed later. I got Diplm the old way, but I also have the same T2/T3 diplm/marauding bug on others toons.